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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        Tool Citations

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        About MultiQC

        This report was generated using MultiQC, version 1.26

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-04-01, 12:35 UTC based on data in: /home/runner/work/pmultiqc/pmultiqc/data

        nf-core/quantms Software Versions

        nf-core/quantms Software Versions are collected at run time from the software output.URL: https://github.com/nf-core/quantms

        Process Name Software Version
        CUSTOM_DUMPSOFTWAREVERSIONS python 3.9.5
        yaml 5.4.1
        FDRIDPEP FalseDiscoveryRate 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        IDFILTER IDFilter 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        IDPEP IDPosteriorErrorProbability 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        IDSCORESWITCHER IDScoreSwitcher 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        MZMLINDEXING FileConverter 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        PROTEOMICSLFQ ProteomicsLFQ 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        SAMPLESHEET_CHECK sdrf-pipelines 0.0.21
        SEARCHENGINEMSGF MSGFPlusAdapter 2.8.0-pre-exported-20220227 Feb 27 2022, 20:31:47
        msgf_plus MS-GF+ Release (v2021.03.22) (22 March 2021)
        Workflow Nextflow 21.10.6
        nf-core/quantms 1.1dev

        nf-core/quantms Workflow Summary

        - this information is collected when the pipeline is started.URL: https://github.com/nf-core/quantms

        Core Nextflow options

        runName
        hungry_linnaeus
        containerEngine
        docker
        launchDir
        /home/chengxin/newPR/quantms
        workDir
        /home/chengxin/newPR/quantms/work
        projectDir
        /home/chengxin/newPR/quantms
        userName
        chengxin
        profile
        test_lfq,docker
        configFiles
        /home/chengxin/newPR/quantms/nextflow.config

        Input/output options

        input
        /home/chengxin/lfq_testdata/BSA_design_urls1.tsv
        outdir
        ./results_lfq

        Protein database

        database
        /home/chengxin/lfq_testdata/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta
        decoy_string
        rev

        Database search

        search_engines
        msgf
        instrument
        N/A

        Modification localization

        luciphor_debug
        N/A

        PSM re-scoring (general)

        posterior_probabilities
        fit_distributions
        run_fdr_cutoff
        0.10

        PSM re-scoring (Percolator)

        description_correct_features
        N/A

        Consensus ID

        consensusid_considered_top_hits
        N/A
        min_consensus_support
        N/A

        Isobaric analyzer

        select_activation
        HCD

        Protein inference

        protein_level_fdr_cutoff
        1.0
        psm_level_fdr_cutoff
        1.0

        Protein Quantification (DDA)

        labelling_type
        label free sample
        ratios
        N/A
        normalize
        N/A
        fix_peptides
        N/A

        DIA-NN

        mass_acc_ms2
        13
        mass_acc_ms1
        7
        scan_window
        8

        Statistical post-processing

        contrasts
        pairwise
        add_triqler_output
        true

        Quality control

        enable_pmultiqc
        true

        Institutional config options

        config_profile_name
        Test profile for DDA LFQ
        config_profile_description
        Minimal test dataset to check pipeline function of the label-free quantification branch of the pipeline

        Max job request options

        max_cpus
        2
        max_memory
        6 GB
        max_time
        2d

        Generic options

        hostnames
        N/A

        MultiQC v1.26 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.